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<title>Per Base GC Content</title>
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<h1>Per Base GC Content</h1>
<h2>Summary</h2>
<p>
Per Base GC Content plots out the GC content of each base
position in a file.
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<p><img src="per_base_gc_content.png"></p>
<p>
In a random library you would expect that there would be little
to no difference between the different bases of a sequence run, so
the line in this plot should run horizontally across the graph. The
overall GC content should reflect the GC content of the underlying
genome.
</p>
<p>
If you see a GC bias which changes in different bases then this 
could indicate an overrepresented sequence which is contaminating
your library.  A bias which is consistent across all bases either
indicates that the original library was sequence biased, or that there
was a systematic problem during the sequencing of the library.
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<h2>Warning</h2>
<p>
This module issues a warning it the GC content of any base strays more
than 5% from the mean GC content.
</p>

<h2>Failure</h2>
<p>
This module will fail if the GC content of any base strays more than 10%
from the mean GC content.
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